void
IoParams::parse(int ac,
char* av[])
{
namespace po = boost::program_options;
typedef std::vector<std::string> StringVectorType;
StringVectorType vItems;
po::options_description desc("Allowed Options");
desc.add_options()
("help", " produce help message")
("out", po::value(&strOut), " output transform file (.tm3d)")
("template", po::value(&strTemplate), " template volume (only for geometry) - if a gcam is present, it needs to be specified")
("subject", po::value(&strSubject), " subject volume (only for geometry)" )
("in", po::value(&vItems)->multitoken(), " input transforms - affine|volume|morph|mesh|gcam + fname")
("dbg", po::value(&vDbgCoords)->multitoken(), " enter debug coordinates ")
;
po::variables_map vm;
po::store( po::parse_command_line(ac,av,desc), vm);
po::notify(vm);
if ( vm.count("help") )
{
std::cout << desc << std::endl;
exit(0);
}
if ( strOut.empty() )
{
std::cerr << " Empty output file name\n";
exit(1);
}
// parse input terms
if ( vItems.empty() )
{
std::cout << " nothing to do - no transforms specified\n";
exit(0);
}
if ( vItems.size() % 2 )
{
std::cerr << " odd number of transform tokens\n";
exit(1);
}
for ( StringVectorType::iterator it = vItems.begin();
it != vItems.end(); )
{
MorphItem item;
item.type = *it++;
item.file = *it++;
this->items.push_back(item);
} // next it
}
void buildImageIntensityModelOnROI(const char* referenceFilename, const char* maskFilename, const char* dir, const char* outputImageFilename) {
typedef itk::PCAModelBuilder<RepresenterType> ModelBuilderType;
typedef itk::StatisticalModel<RepresenterType> StatisticalModelType;
typedef std::vector<std::string> StringVectorType;
typedef itk::DataManager<RepresenterType> DataManagerType;
RepresenterType::Pointer representer = RepresenterType::New();
typedef itk::ImageFileReader< ImageType > MaskReaderType;
MaskReaderType::Pointer maskReader = MaskReaderType::New();
maskReader->SetFileName( maskFilename );
maskReader->Update();
representer->SetReference( ReadImageFromFile(referenceFilename), maskReader->GetOutput() );
StringVectorType filenames;
getdir(dir, filenames, ".vtk");
DataManagerType::Pointer dataManager = DataManagerType::New();
dataManager->SetRepresenter(representer);
for (StringVectorType::const_iterator it = filenames.begin(); it != filenames.end(); it++) {
std::string fullpath = (std::string(dir) + "/") + *it;
dataManager->AddDataset( ReadImageFromFile(fullpath), fullpath.c_str());
}
ModelBuilderType::Pointer pcaModelBuilder = ModelBuilderType::New();
StatisticalModelType::Pointer model = pcaModelBuilder->BuildNewModel(dataManager->GetSampleDataStructure(), 0);
std::cout<<"dimensionality of the data: "<<model->GetDomain().GetNumberOfPoints()<<", dimension of the images: "<<(*dataManager->GetSampleDataStructure().begin())->GetSample()->GetLargestPossibleRegion().GetNumberOfPixels()<<std::endl;
std::cout<<"writing the mean sample to a png file..."<<std::endl;
typedef itk::ImageFileWriter< ImageType > ImageWriterType;
ImageWriterType::Pointer writer = ImageWriterType::New();
writer->SetFileName( outputImageFilename );
writer->SetInput(model->DrawSample());
writer->Update();
}